benchmark deleted

inputs

@@ -1,33 +1,23 @@
 {
-  "{{ project_name }}.benchmarking_dir": "oss://chinese-quartet/quartet-result-data/NCTR_benchmarking_20181215/",
-  "{{ project_name }}.vcfstat.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-hap:latest",
   "{{ project_name }}.qualimap.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/qualimap:2.0.0",
   "{{ project_name }}.qualimap.cluster_config": "OnDemand bcs.a2.7xlarge img-ubuntu-vpc",
   "{{ project_name }}.fasta": "GRCh38.d1.vd1.fa",
   "{{ project_name }}.fastqc.disk_size": "150",
   "{{ project_name }}.mergeSentieon.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/gatk:v2019.01",
-  "{{ project_name }}.benchmark.cluster_config": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc",
   "{{ project_name }}.sentieon.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/gatk:v2019.01",
   "{{ project_name }}.fastqscreen.cluster_config": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc",
   "{{ project_name }}.fastqc.cluster_config": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc",
-  "{{ project_name }}.benchmark.disk_size": "150",
-  "{{ project_name }}.vcfstat.disk_size": "100",
   "{{ project_name }}.fastqc.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastqc:v0.11.5",
   "{{ project_name }}.sentieon.cluster_config": "OnDemand bcs.a2.large img-ubuntu-vpc",
-  "{{ project_name }}.benchmark.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-hap:latest",
   "{{ project_name }}.inputSamplesFile": "{{ inputSamplesFile }}",
   "{{ project_name }}.fastqscreen.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastqscreen:0.12.0",
-  "{{ project_name }}.mergeNum.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/gatk:v2019.01",
   "{{ project_name }}.screen_ref_dir": "oss://pgx-reference-data/fastq_screen_reference/",
-  "{{ project_name }}.mergeNum.disk_size": "100",
   "{{ project_name }}.fastq_screen_conf": "oss://pgx-reference-data/fastq_screen_reference/fastq_screen.conf",
   "{{ project_name }}.multiqc.cluster_config": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc",
   "{{ project_name }}.qualimap.disk_size": "500",
   "{{ project_name }}.multiqc.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/multiqc:v1.8",
-  "{{ project_name }}.mergeNum.cluster_config": "OnDemand bcs.a2.large img-ubuntu-vpc",
   "{{ project_name }}.mergeSentieon.disk_size": "100",
   "{{ project_name }}.sentieon.disk_size": "100",
-  "{{ project_name }}.vcfstat.cluster_config": "OnDemand bcs.a2.large img-ubuntu-vpc",
   "{{ project_name }}.mergeSentieon.cluster_config": "OnDemand bcs.a2.large img-ubuntu-vpc",
   "{{ project_name }}.fastqscreen.disk_size": "100",
   "{{ project_name }}.multiqc.disk_size": "100",

tasks/mergeSentieon.wdl

@@ -18,10 +18,10 @@ task mergeSentieon {
 	command <<<
 		set -o pipefail
 		set -e
-		cat ${aln_metrics_header} | sed -n '1,1p' | cat - ${aln_metrics_data} > aln_metrics.txt
-		cat ${dedup_metrics_header} | sed -n '1,1p' | cat - ${dedup_metrics_data} > dedup_metrics.txt
-		cat ${is_metrics_header} | sed -n '1,1p' | cat - ${is_metrics_data} > is_metrics.txt
-		cat ${deduped_coverage_header} | sed -n '1,1p' | cat - ${deduped_coverage_data} > deduped_coverage.txt
+		cat ${aln_metrics_header} | sed -n '1,1p' | cat - ${sep=" " aln_metrics_data} > aln_metrics.txt
+		cat ${dedup_metrics_header} | sed -n '1,1p' | cat - ${sep=" " dedup_metrics_data} > dedup_metrics.txt
+		cat ${is_metrics_header} | sed -n '1,1p' | cat - ${sep=" " is_metrics_data} > is_metrics.txt
+		cat ${deduped_coverage_header} | sed -n '1,1p' | cat - ${sep=" " deduped_coverage_data} > deduped_coverage.txt
 	>>>
 
 	runtime {

tasks/multiqc.wdl

@@ -8,8 +8,6 @@ task multiqc {
 
 	Array[File] zip
 
-	Array[File] summary
-
 	String docker
 	String cluster_config
 	String disk_size
@@ -20,11 +18,9 @@ task multiqc {
 		mkdir -p /cromwell_root/tmp/fastqc
 		mkdir -p /cromwell_root/tmp/fastqscreen
 		mkdir -p /cromwell_root/tmp/bamqc
-		mkdir -p /cromwell_root/tmp/benchmark
 
 		cp ${sep=" " read1_zip} ${sep=" " read2_zip} /cromwell_root/tmp/fastqc
 		cp ${sep=" " txt1} ${sep=" " txt2} /cromwell_root/tmp/fastqscreen
-		cp ${sep=" " summary} /cromwell_root/tmp/benchmark
 		for i in ${sep=" " zip}
 		do
 		  tar -zxvf $i -C /cromwell_root/tmp/bamqc

workflow.wdl

@@ -1,21 +1,17 @@
 import "./tasks/fastqc.wdl" as fastqc
 import "./tasks/fastqscreen.wdl" as fastqscreen
 import "./tasks/qualimap.wdl" as qualimap
-import "./tasks/benchmark.wdl" as benchmark
-import "./tasks/vcfstat.wdl" as vcfstat
 import "./tasks/sentieon.wdl" as sentieon
 import "./tasks/multiqc.wdl" as multiqc
-import "./tasks/mergeNum.wdl" as mergeNum
 import "./tasks/mergeSentieon.wdl" as mergeSentieon
 
 
-workflow {{ project_name }} {
+workflow project_name {
 
 	File inputSamplesFile
 	Array[Array[File]] inputSamples = read_tsv(inputSamplesFile)
 	File screen_ref_dir
 	File fastq_screen_conf
-	File benchmarking_dir
 	File ref_dir
 	String fasta
 
@@ -40,22 +36,6 @@ workflow {{ project_name }} {
 			bai=sample[3]
 		}
 
-		call benchmark.benchmark as benchmark {
-			input:
-			vcf=sample[4],
-			benchmarking_dir=benchmarking_dir,
-			ref_dir=ref_dir,
-			sample_mark=sample[5],
-			fasta=fasta
-		}
-
-		call vcfstat.vcfstat as vcfstat {
-			input:
-			rtg_vcf=benchmark.rtg_vcf,
-			rtg_vcf_index=benchmark.rtg_vcf_index,
-			sample_name=sample[6]
-		}
-
 		call sentieon.sentieon as sentieon {
 			input:
 			aln_metrics=sample[7],
@@ -72,13 +52,7 @@ workflow {{ project_name }} {
 		read2_zip=fastqc.read2_zip,
 		txt1=fastqscreen.txt1,
 		txt2=fastqscreen.txt2,
-		zip=qualimap.zip,
-		summary=benchmark.summary
-	}
-
-	call mergeNum.mergeNum as mergeNum {
-		input:
-		vcfnumber=vcfstat.vcfnumber
+		zip=qualimap.zip
 	}
 
 	call mergeSentieon.mergeSentieon as mergeSentieon {